Sat Oct 8 22:47:30 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 22:47:30 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5459202 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.78700 40.65800 ymin,ymax (A): 16.42900 76.28700 zmin,zma (A): 22.74600 87.95700 x,y,z range (A): 56.44500 59.85800 65.21100 scale (grids/A): 0.5459202 object centre (A): 12.43550 46.35800 55.35150 number of atom coordinates read : 3322 total number of charged atoms : 3180 net assigned charge : 14.22602 assigned positive charge : 488.8647 centred at (gu) : 89.88939 90.19333 91.12450 assigned negative charge : -474.6404 centred at (gu) : 89.76199 90.25866 91.30453 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6646 nv = 96 ne = 84 npr = 64902 no. pairs analyzed = 64902 no. exposed pairs = 4377 no. arc points = 31710 no. surface atoms = 1461 nbur = 1861 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 274 mr = 3328 m= 0 mr = 14 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2300000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3170 ## 407 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8615 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6297254E-09 -5.4647320E-10 midg,1,midg; midg,igrid,midg 1.2984250E-09 4.5721291E-10 1,midg,midg; igrid,midg,midg -1.3549189E-11 1.7413182E-09 gauss-seidel spectral radius is 0.9827397 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 22:47:31 rms-change max change #iterations 7.5034194E-02 12.74161 at 10iterations 5.0094635E-03 0.7291468 at 20iterations 3.6838214E-04 5.2350998E-02 at 30iterations 3.7679481E-05 5.0711632E-03 at 40iterations 6.1800215E-06 6.5243244E-04 at 50iterations finished qdiffx linear iterations at : 22:47:34 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 6.1800215E-06 6.5243244E-04 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 22:47:35 3.749u 0.214s 0:04.28 92.2% 0+0k 0+0io 6pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 22:47:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.637761 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.78700 40.65800 ymin,ymax (A): 16.42900 76.28700 zmin,zma (A): 22.74600 87.95700 x,y,z range (A): 56.44500 59.85800 65.21100 scale (grids/A): 1.637761 object centre (A): 12.43550 46.35800 55.35150 number of atom coordinates read : 3322 total number of charged atoms : 3180 net assigned charge : 14.22602 assigned positive charge : 488.8647 centred at (gu) : 89.66750 90.57939 93.37239 assigned negative charge : -474.6404 centred at (gu) : 89.28584 90.77565 93.91329 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22919 mr = 48793 m= 2405 mr = 15682 m= 71 mr = 1132 m= 0 mr = 6 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 589 time to turn everything in is 0.3700000 number of dielectric boundary points 33304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 24372 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5459202 object centre at (A) : 12.43550 46.35800 55.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6440479E-02 6.1470750E-03 midg,1,midg; midg,igrid,midg 2.6638748E-02 1.4538040E-02 1,midg,midg; igrid,midg,midg -2.9864009E-03 1.1248389E-02 gauss-seidel spectral radius is 0.9982490 estimated iterations to convergence 190 setup time was (sec) 0.6100000 now iterating at: 22:47:36 rms-change max change #iterations 3.490270 152.0554 at 10iterations 1.462770 55.10905 at 20iterations 0.6210375 22.68195 at 30iterations 0.2620385 9.045994 at 40iterations 0.1104613 3.732042 at 50iterations 4.7049481E-02 1.703186 at 60iterations 1.9807823E-02 0.6752672 at 70iterations 8.3736153E-03 0.2981606 at 80iterations 3.5452845E-03 0.1205151 at 90iterations 1.5017354E-03 4.9665451E-02 at 100iterations 6.3900941E-04 2.1600723E-02 at 110iterations 2.7071798E-04 8.9468956E-03 at 120iterations finished qdiffx linear iterations at : 22:47:43 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 2.7071798E-04 8.9468956E-03 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 22:47:44 8.643u 0.278s 0:09.54 93.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 22:47:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.456641 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.78700 40.65800 ymin,ymax (A): 16.42900 76.28700 zmin,zma (A): 22.74600 87.95700 x,y,z range (A): 56.44500 59.85800 65.21100 scale (grids/A): 2.456641 object centre (A): 12.43550 46.35800 55.35150 number of atom coordinates read : 3322 total number of charged atoms : 3180 net assigned charge : 14.22602 assigned positive charge : 488.8647 centred at (gu) : 89.50097 90.86900 95.05843 assigned negative charge : -474.6404 centred at (gu) : 88.92883 91.16334 95.86996 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78459 mr = 119845 m= 22874 mr = 61516 m= 3691 mr = 17144 m= 280 mr = 2380 m= 7 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2082 time to turn everything in is 0.9600000 number of dielectric boundary points 75135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 25402 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.637761 object centre at (A) : 12.43550 46.35800 55.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4371852 7.3764615E-02 midg,1,midg; midg,igrid,midg 0.4519052 0.3399268 1,midg,midg; igrid,midg,midg -2.5003109E-02 0.1636670 gauss-seidel spectral radius is 0.9991730 estimated iterations to convergence 275 setup time was (sec) 1.280000 now iterating at: 22:47:46 rms-change max change #iterations 9.031965 333.7148 at 10iterations 5.156367 150.0042 at 20iterations 2.927350 85.84906 at 30iterations 1.651992 49.22607 at 40iterations 0.9295509 20.17584 at 50iterations 0.5234725 11.12428 at 60iterations 0.2922157 6.443976 at 70iterations 0.1634934 3.885866 at 80iterations 9.1528125E-02 1.855477 at 90iterations 5.0938860E-02 1.173452 at 100iterations 2.8397290E-02 0.5740948 at 110iterations 1.5844973E-02 0.3240209 at 120iterations 8.8330992E-03 0.1783409 at 130iterations 4.9109426E-03 9.2665672E-02 at 140iterations 2.7309647E-03 5.4183960E-02 at 150iterations 1.5197827E-03 3.1138420E-02 at 160iterations 8.4741670E-04 1.6087532E-02 at 170iterations 4.7016196E-04 8.9054108E-03 at 180iterations finished qdiffx linear iterations at : 22:47:59 total time elapsed so far: 14.21000 # loops : 180 mean,max change (kT/e) : 4.7016196E-04 8.9054108E-03 energy calculations done at 14.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.34000 DelPhi exited at 22:48:00 14.341u 0.320s 0:15.67 93.5% 0+0k 0+0io 0pf+0w